更新于：2024-05-01

CLP1

cleavage factor polyribonucleotide kinase subunit 1

更新于：2024-05-01

基本信息

别名

cleavage factor polyribonucleotide kinase subunit 1、CLP1、hClp1

+ [5]

简介

Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3'-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA (PubMed:24766809, PubMed:24766810). Its role in tRNA splicing and maturation is required for cerebellar development (PubMed:24766809, PubMed:24766810). Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing.

关联

100 项与 CLP1 相关的临床结果

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100 项与 CLP1 相关的转化医学

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0 项与 CLP1 相关的专利（医药）

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135

项与 CLP1 相关的文献（医药）

2024-02-13·BMC medical genomics

Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review.

Article

作者: Mohammad-Reza Ghasemi ; Sahand Tehrani Fateh ; Aysan Moeinafshar ; Hossein Sadeghi ; Parvaneh Karimzadeh ; Reza Mirfakhraie ; Mitra Rezaei ; Farzad Hashemi-Gorji ; Morteza Rezvani Kashani ; Fatemehsadat Fazeli Bavandpour ; Saman Bagheri ; Parinaz Moghimi ; Masoumeh Rostami ; Rasoul Madannejad ; Hassan Roudgari ; Mohammad Miryounesi

BACKGROUND:

Pontocerebellar hypoplasia is an umbrella term describing a heterogeneous group of prenatal neurodegenerative disorders mostly affecting the pons and cerebellum, with 17 types associated with 25 genes. However, some types of PCH lack sufficient information, which highlights the importance of investigating and introducing more cases to further elucidate the clinical, radiological, and biochemical features of these disorders. The aim of this study is to provide an in-depth review of PCH and to identify disease genes and their inheritance patterns in 12 distinct Iranian families with clinically confirmed PCH.

METHODS:

Cases included in this study were selected based on their phenotypic and genetic information available at the Center for Comprehensive Genetic Services. Whole-exome sequencing (WES) was used to discover the underlying genetic etiology of participants' problems, and Sanger sequencing was utilized to confirm any suspected alterations. We also conducted a comprehensive molecular literature review to outline the genetic features of the various subtypes of PCH.

RESULTS:

This study classified and described the underlying etiology of PCH into three categories based on the genes involved. Twelve patients also were included, eleven of whom were from consanguineous parents. Ten different variations in 8 genes were found, all of which related to different types of PCH. Six novel variations were reported, including SEPSECS, TSEN2, TSEN54, AMPD2, TOE1, and CLP1. Almost all patients presented with developmental delay, hypotonia, seizure, and microcephaly being common features. Strabismus and elevation in lactate levels in MR spectroscopy were novel phenotypes for the first time in PCH types 7 and 9.

CONCLUSIONS:

This study merges previously documented phenotypes and genotypes with unique novel ones. Due to the diversity in PCH, we provided guidance for detecting and diagnosing these heterogeneous groups of disorders. Moreover, since certain critical conditions, such as spinal muscular atrophy, can be a differential diagnosis, providing cases with novel variations and clinical findings could further expand the genetic and clinical spectrum of these diseases and help in better diagnosis. Therefore, six novel genetic variants and novel clinical and paraclinical findings have been reported for the first time. Further studies are needed to elucidate the underlying mechanisms and potential therapeutic targets for PCH.

2023-08-22·Journal of molecular evolution

Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei.

Article

作者: Motofumi Saito ; Rerina Inose ; Asako Sato ; Masaru Tomita ; Haruo Suzuki ; Akio Kanai

The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5' end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species to classify the diverse Clp1 family proteins. The average number of Clp1 family proteins in eukaryotes was 2.3 ± 1.0, and most representative species had both Clp1 and Nol9/Grc3 proteins, suggesting that the Clp1 and Nol9/Grc3 groups were already formed in the eukaryotic ancestor by gene duplication. We also detected an average of 4.1 ± 0.4 Clp1 family proteins in members of the protist phylum Euglenozoa. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. As in this example, N-terminal and C-terminal domain replacement also contributed to the diversification of the Clp1 family proteins in other eukaryotic species. Our analysis also revealed that the Clp1 family proteins in humans and plants diversified through isoforms created by alternative splicing.

2023-05-25·Nature structural & molecular biology

Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN.

Article

作者: Samoil Sekulovski ; Lukas Sušac ; Lukas S Stelzl ; Robert Tampé ; Simon Trowitzsch

Heterotetrameric human transfer RNA (tRNA) splicing endonuclease TSEN catalyzes intron excision from precursor tRNAs (pre-tRNAs), utilizing two composite active sites. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH). Despite the essential function of TSEN, the three-dimensional assembly of TSEN-CLP1, the mechanism of substrate recognition, and the structural consequences of disease mutations are not understood in molecular detail. Here, we present single-particle cryogenic electron microscopy reconstructions of human TSEN with intron-containing pre-tRNAs. TSEN recognizes the body of pre-tRNAs and pre-positions the 3' splice site for cleavage by an intricate protein-RNA interaction network. TSEN subunits exhibit large unstructured regions flexibly tethering CLP1. Disease mutations localize far from the substrate-binding interface and destabilize TSEN. Our work delineates molecular principles of pre-tRNA recognition and cleavage by human TSEN and rationalizes mutations associated with PCH.

项与 CLP1 相关的新闻（医药）

2023-05-30

·生物探索

Molecular Cell | 西湖大学施一公团队再获新进展！解析人类pre-tRNA剪接机制，完善剪接体结构「地图」

从tRNA前体 (pre-tRNA)中去除内含子在生命的三个王国中都是必不可少的。在人类中，这一过程是由tRNA剪接内切酶(TSEN)介导的，包括四个亚基：TSEN2、TSEN15、TSEN34和TSEN54。2023年4月6日，西湖大学施一公团队在Molecular Cell （IF=19）在线发表题为“Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease”的研究论文，该研究揭示了人tRNA剪接核酸内切酶去除tRNA前体内含子的结构基础。该研究报道了人TSEN在催化前和催化后的平均分辨率分别为2.94和2.88 Å下与全长pre-tRNA结合的冷冻电镜结构。人体TSEN具有一个延伸的表面凹槽，容纳l型的pre-tRNA。pretRNA的成熟结构域由TSEN34、TSEN54和TSEN2的保守结构元素识别。这种识别定位pre-tRNA的反密码子茎，并将30剪接位点和50剪接位点分别放置在TSEN34和TSEN2的催化中心。大部分内含子序列与TSEN没有直接的相互作用，这解释了为什么不同内含子的pre-tRNAs可以被容纳和裂解。该结构揭示了TSEN pre-tRNA裂解的分子尺机制。转运RNA (tRNA)对于遗传信息的流动至关重要，它允许核糖体将mRNA翻译成蛋白质。成熟tRNAs是由tRNAs前体 (pre-tRNAs)通过一系列转录后处理和修饰步骤生成的。在生命的三个王国中，对于pre-tRNAs的一个子集，内含子序列都存在，必须通过剪接去除。在人类基因组中预测的tRNA基因中，至少有28个含有长度和序列不同的内含子。在古生菌和真核生物中，内含子通过tRNA剪接内切酶(TSENs)去除，然后通过涉及特定tRNA连接酶的多步骤过程连接两个释放的外显子。真核生物TSEN包括两个催化亚基TSEN34和TSEN2，两个结构亚基TSEN54和TSNE15，TSEN34和TSEN2分别在30剪接位点(30SS)和50剪接位点(50SS)切割pre-tRNA。在哺乳动物中，多核苷酸激酶CLP1与TSEN共纯化。尽管CLP1在体外tRNA切割前是可有可无的，但CLP1和所有TSEN亚基的突变已与tRNA代谢改变和神经病变相关。机理模式图（图源自Molecular Cell ）自从20世纪70年代发现tRNA内含子以来，广泛的生化和晶体学研究中对各种类型的TSENs的pre-tRNA裂解有了相当大的了解。特别地，古生菌TSEN与隆起-螺旋-隆起(BHB) RNA基序复合物的结构揭示了一些关键的相互作用，这些相互作用是pre-tRNA识别和切割所必需的。然而，关于真核生物TSEN的结构信息出现缓慢，严重限制了对pre-tRNA裂解机制的理解。例如，TSEN被认为采用分子尺机制来识别pre-tRNA的两位点切割，但由于缺乏被TSEN结合的全长pre-tRNA的结构信息，其基础仍不充分。此外，四个TSEN亚基是如何被组织成一个完整的、具有两个独立活性位点的内切酶的仍不清楚。该研究报道了人类TSEN与全长pre-tRNA结合的两个高分辨率结构：一个处于催化前状态，另一个处于催化后状态。为了捕捉预催化状态，作者在TSEN中引入了两个错意突变：TSEN34中的H255A和TSNE中的H377A。总之，该研究的人类TSEN/CLP1/pretRNA复合物在催化前和催化后状态下的结构为理解pre-tRNA剪接的机制提供了一个框架。本文转载自“iNature”公众号。校对|风立宵End 往期精选围观 ‍把病毒困在“陷阱”里！海德堡大学探明病毒渗透最后一步，或将带来预防新手段！热文基因振荡器：在两种衰老模式间来回切换，细胞寿命延长了82%！热文用超声波突破皮肤屏障！MIT科学家为皮肤给药提供可穿戴解决方案热文新发现：加速癌症发展的染色体外DNA，甚至出现在癌症之前，推动组织癌变！热文在基因组中“跳来跳去”的转座子，有望成为免疫疗法抗击肿瘤的新靶点！点击“阅读原文”，了解更多~

临床结果信使RNA抗体药物偶联物

2023-04-10

·生物谷

Mol Cell：施一公团队解析人类pre-tRNA剪接机制，完善剪接体结构地图

目前，施一公团队克服技术障碍，深入探索生命细节，获得人类TSEN/CLP1/pretRNA复合物在催化前和催化后状态下的结构，为理解pre-tRNA剪接的机制提供了一个全新的框架。长久以来，剪接体的调控机理是怎样的，它们在细胞内部的动态组合和变化是怎样的，深深地吸引着科学家们的研究兴趣，但其神秘的面纱一直未被揭开。 2023年4月6日，西湖大学施一公团队在 Molecular Cell 期刊发表了题为：Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease 的研究论文。该研究首次解析了人类tRNA剪接内切核酸酶（TSEN）在催化前和催化后状态下与全长tRNA前体（pre-tRNA）结合的低温电子显微镜结构，显示了TSEN如何识别pre-tRNA，并将3'剪接位点和5'剪接位点定位到其切割位点，综合利用结构生物学和生化工作解释了人类TSEN去除pre-tRNA内含子的分子机制。转运RNA（tRNA）对生物遗传信息的传递至关重要，它通过核糖体将mRNA翻译成蛋白质。成熟的tRNAs由前体tRNAs（pre-tRNAs）通过一系列的转录后加工和修饰步骤产生，从pre-tRNA中去除内含子对于生物遗传进化是必不可少的。在人类中，去除pre-tRNA中内含子的过程是由tRNA剪接内切核酸酶（TSEN）介导的，该亚酶包括四个亚基：TSEN2、TSEN15、TSEN34 和 TSEN54。值得一提的是，尽管多核苷酸激酶CLP1在体外对前tRNA切割是可有可无的，但CLP1中的突变和所有TSEN亚基都与tRNA代谢和神经病理学的改变有关。为回答pre-tRNA是如何被TSEN识别的，以及5'剪接位点和3'剪接位点是如何被加载到TSEN2/TSEN34的活性位点这两个困扰科研界多年的谜题，该研究通过纯化人TSEN/CLP1复合物、pre-tRNA切割试验、TSEN/CLP1/前pre-tRNA复合体的组装、冷冻电镜样品制备和数据采集以及竞争性结合测定生化实验，对其进行深入探索。本研究首次报道了两种人类TSEN与全长pre-tRNA结合、高分辨率低温电子显微镜结构：一种在催化前状态，另一种在催化后状态，平均分辨率分别高达2.94Å和2.88Å。研究结果显示人类TSEN的结构特征是一个延伸的表面凹槽，容纳了l形的pre-tRNA，pre-tRNA的成熟结构域被TSEN34、TSEN54和TSEN2的保守结构元件所识别，这种识别定位了pre-tRNA的反密码子茎。令人惊喜的是，5'剪接位点和3'剪接位点周围的核苷酸主要被TSEN2和TSEN34识别，这些相互作用可以确保5'剪接位点和3'剪接位点分别精确地放置在TSEN2和TSEN34的催化中心中。此外，为了捕获预催化状态，研究人员在TSEN中引入了两个错义突变：TSEN34中的H255A和TSNE2中的H377A，进而研究其结构信息以及结构引导的生化分析，为成功解析人类TSEN前tRNA识别和切割的机制提供了基础。考虑到pre-tRNA和tRNA结构的相似性，TSEN延伸的扩展表面凹槽也应该识别tRNA。为证实该分析，tRNAARG-UCU与TSEN/CLP1形成了一个稳定的复合物。与tRNA相比，pre-tRNA可以被TSEN识别，其更具体的相互作用指向其独特的BHL基序。上述结果充分地解释了为什么大部分的内含子序列与TSEN没有直接的相互作用，而不同内含子的pre-tRNA可以被容纳和裂解，解析了人类TSEN去除pre-tRNA内含子的分子机制。值得一提的是，施一公及张晓峰团队于两个月前发表的研究论文：Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly，揭秘三种RNA解旋酶作用机制——人U2 snRNP组装中RNA解旋酶DDX42和DDX46的作用机制，为癌症突变机制提供新见解。施一公院士团队是世界上首个、也是唯一一个成功捕获并解析了RNA剪接过程中所有完全组装剪接体高分辨率三维结构系列成果的团队。从组装到被激活，从两步转酯反应发生到剪接体的解聚，各种各样状态的剪接体完整覆盖了剪接通路，首次将剪接体介导的RNA剪接过程完整地串联起来，为理解RNA剪接的分子机理提供了最清晰、最全面的结构信息，成功获取剪接体这颗分子生物学皇冠上的明珠。图 5：剪接体结构汇总（来源：https://ygshi.org/research）目前，施一公团队克服技术障碍，深入探索生命细节，获得人类TSEN/CLP1/pretRNA复合物在催化前和催化后状态下的结构，为理解pre-tRNA剪接的机制提供了一个全新的框架。如此振奋人心的研究结果令人看到了科学家们孜孜不倦的努力，从基础科学的研究到临床应用，再到治疗疾病，未来可期。

信使RNA临床结果抗体药物偶联物

2023-04-07

·生物谷

Molecular Cell：施一公团队揭示人源tRNA剪接内切酶识别和剪切前体tRNA内含子的分子机理

北京时间2023年4月6日，西湖大学生命科学学院施一公团队在《分子细胞》(Molecular Cell) 在线发表了题为“Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease”的最新研究论文，报道了pre-tRNA结合人源tRNA剪接内切酶 (tRNA splicing endonuclease, TSEN) 复合物处于“预催化”和“催化后”两种状态的高分辨率结构，结合体外生化，揭示了TSEN复合物识别和剪切pre-tRNA内含子的分子机理。论文链接：https://www-cell-com.libproxy1.nus.edu.sg/molecular-cell/fulltext/S1097-2765(23)00205-8tRNA是生物遗传信息传递“中心法则”的重要参与者[1]。作为蛋白质翻译过程的解码器，tRNA负责将mRNA中的遗传信息精确地对应到蛋白质序列中。在tRNA合成过程中，前体tRNA (precursor tRNA, pre-tRNA) 需要经过一系列转录后加工和修饰，才能生成成熟的tRNA。其中一个重要的过程是“tRNA剪接”[2]。在所有的生物中，均有一部分pre-tRNA存在内含子。这些内含子序列必须经过tRNA剪接被精确地去除[3]。在真核生物中，tRNA剪接分为“剪”和“接”两个过程：前者负责将pre-tRNA中的内含子去除，由TSEN复合物执行；后者负责将切开的两个外显子连接，由 tRNA 连接酶复合物介导[4] (图1) 。这两个过程的精确进行对 tRNA 的正确折叠和稳定性，以及对蛋白质合成的效率和精度都至关重要。其功能异常会导致部分密码子无法解码，从而引起蛋白质合成紊乱，并最终引发包括癌症、神经系统疾病和发育缺陷在内的多种人类疾病[5]。由于缺乏关键的结构信息，长期以来人们对pre-tRNA剪接机理的理解较为滞后。其中一个关键的科学问题是TSEN复合物如何准确识别在序列上并不保守的pre-tRNA，并在相应的剪接位点完成内含子的剪切？图1 tRNA剪接过程示意图研究人员首先纯化出性质均一的人源TSEN/CLP1复合物，然后建立体外剪切反应，用于组装TSEN/CLP1/pre-tRNA复合物。通过在TSEN催化亚基的活性位点引入突变的方法，成功捕获了该复合物处于“预催化”和“催化后”的两种状态，并利用冷冻电镜技术解析了相应的结构 (图2) 。两种状态的TSEN/CLP1/pre-tRNA复合物的整体结构十分相似，但在“催化后”状态中，pre-tRNA的剪接位点已经完成了剪切反应。图2 TSEN/pre-tRNA复合物预催化与催化后状态的电镜结构通过结构分析，研究人员发现TSEN复合物的四个亚基组装形成了一个连续的表面凹槽，非常适合容纳L形的pre-tRNA底物。在“预催化”状态中，pre-tRNA的成熟结构域和反密码子茎被TSEN34、TSEN54和TSEN2识别。这些相互作用将3’剪接位点 (3’-splice site, 3’SS) 导向TSEN34的催化中心，并且pre-tRNA在3’SS附近的磷酸骨架发生约180度的翻转，形成一个凸起 (3’SS bulge) ，使得3’SS更加靠近TSEN34的催化中心。5’剪接位点 (5’-splice site, 5’SS) 位于反密码子 (anticodon) 下游的一个核苷酸，反密码子与内含子的部分序列通过碱基配对，形成A-I螺旋 (Anticodon-intron helix) 。一旦成熟结构域和反密码子茎被TSEN识别，在A-I螺旋的引导下，5’SS也会随之定向到TSEN2的催化中心。大部分内含子序列不参与pre-tRNA与TSEN的相互作用，解释了为什么内含子长度、序列各不相同的pre-tRNA可以被TSEN结合和剪切。总的来说，这些结构上的发现以及基于结构的生化分析，共同揭示了TSEN复合物识别、剪切pre-tRNA的分子机制。这也是施一公团队在mRNA剪接之外，探究另一类特殊内含子的剪接机理的一项重要工作。西湖大学生命科学学院施一公教授为本文的通讯作者，原西湖大学助理研究员张晓峰（现为中国科学技术大学研究员）为本文的共同通讯作者。张晓峰、西湖大学博士生杨丰华、副研究员占谢超和博士生卞彤为本文的共同第一作者。西湖大学博士生邢芷涵、卢怡辰参与了本研究的部分工作。本研究得到了西湖大学冷冻电镜平台、高性能计算中心、晶体学平台、质谱与代谢组学平台的大力支持。本研究获得了国家自然科学基金委、西湖教育基金会、西湖大学、西湖实验室、中国博士后科学基金、博士后创新人才计划的相关经费支持。参考文献：[1] CRICK F H C. Origin of Genetic Code [J]. J Mol Biol, 1968, 38(3): 367-&.[2] ABELSON J, TROTTA C R, LI H. tRNA splicing [J]. J Biol Chem, 1998, 273(21): 12685-8.[3] PARISIEN M, WANG X, PAN T. Diversity of human tRNA genes from the 1000-genomes project [J]. RNA Biol, 2013, 10(12): 1853-67.[4] HAYNE C K, LEWIS T A, STANLEY R E. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex [J]. Wiley Interdiscip Rev RNA, 2022: e1717.[5] SEKULOVSKI S, DEVANT P, PANIZZA S, et al. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia [J]. Nat Commun, 2021, 12(1): 5610.

临床结果信使RNA抗体药物偶联物